I wonder though if this quote is more in reference to how they meet. I can imagine a story where Waynetec and Lexcorps are working together to find a way to take down Superman or beings like him in the case of a future invasion. It would be logical that Batman might even consider Superman a conspirator in the alien attack and set out to take him down at the beginning of the movie, only to join forces with him as the story progresses. This is still in very early stages so I wouldn't read to much in to the DKR reference just yet. On another note, Super-hero movies are perfect to set up like a James Bond series. There is not much difference between a different actor in a movie and a new creative team on a comic when you think about it.